[BioC] segfault with rmaMicroRna in AgiMicroRna package

[Seth Falcon]

Heyi,

A couple of suggestions to help you get help more quickly.

1. Try upgrading your R and Bioconductor packages to the latest release 
and see if that resolves the problem for you.

2. If you still see the crash, since you are running on Linux you should 
be able to extract some further debugging information that will be 
useful to the package maintainer.  Do as follows:

    bash$ R -d gdb
    (gdb) run
       R> # run your example to get the crash
    (gdb) bt 15

Send the output of the backtrace to help identify where things are going 
astray.

+ seth


On 4/30/10 3:48 PM, heyi xiao wrote:
>
>
>
>
> Dear Pedro,
>
> I am using AgiMicroRna 1.0.0 to process my agilent miRNA
> microarray data. Agilent Feature Extraction Software v10.7 was
> used to extract the features. I got segfault when I do rmaMicroRna:
>
>
>
>> dd.rma=rmaMicroRna(dd.micro,
>
> +  normalize=TRUE,
>
> +  background=TRUE)
>
>
>
>   *** caught segfault ***
>
> address 0x10cd6000,
> cause 'memory not mapped'
>
>
>
> However, this
> problem is gone when I do rmaMicroRna on a subset of my dd.micro:
>
>> dd.rma=rmaMicroRna(dd.micro[,13:16],
>
> +  normalize=TRUE,
>
> +  background=TRUE)
>
>
>
> I have check my dd.micro
> data, everything is fine. In other words, rmaMicroRna only works when I apply
> it to a smaller dataset. BTW, I am using a 64 bit version of R on linux
> machine. Therefore, memory limit shouldn’t be an issue here. Could you look at
> this issue? Thanks a lot!
>
> Heyi
>
>
>
> PS: my session information:
>
>> sessionInfo()
>
> R version 2.9.0
> (2009-04-17)
>
> x86_64-unknown-linux-gnu
>
>
>
>
> locale:
>
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
>
>
> attached base
> packages:
>
> [1] stats     graphics
> grDevices utils     datasets  methods
> base
>
>
>
> other attached
> packages:
>
> [1] AgiMicroRna_1.0.0
> preprocessCore_1.6.0 affy_1.22.0
>
>
> [4] limma_2.18.0
> Biobase_2.4.1
>
>
>
> loaded via a
> namespace (and not attached):
>
> [1] affyio_1.12.0
>
>
>
>
>
> 	[[alternative HTML version deleted]]
>
>
>
>
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-- 
Seth Falcon
Bioconductor Core Team | FHCRC